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Items: 1 to 20 of 57

1.

Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150.

PMID:
27854363
2.

Conpair: concordance and contamination estimator for matched tumor-normal pairs.

Bergmann EA, Chen BJ, Arora K, Vacic V, Zody MC.

Bioinformatics. 2016 Oct 15;32(20):3196-3198.

3.

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia.

Bacharach E, Mishra N, Briese T, Zody MC, Kembou Tsofack JE, Zamostiano R, Berkowitz A, Ng J, Nitido A, Corvelo A, Toussaint NC, Abel Nielsen SC, Hornig M, Del Pozo J, Bloom T, Ferguson H, Eldar A, Lipkin WI.

MBio. 2016 Apr 5;7(2):e00431-16. doi: 10.1128/mBio.00431-16.

4.

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, Hanna D, Swanson JM, Faustman EM, Bamshad MJ, Stamatoyannopoulos J, Nickerson DA, McCallion AS, Darnell R, Eichler EE.

Am J Hum Genet. 2016 Jan 7;98(1):58-74. doi: 10.1016/j.ajhg.2015.11.023.

5.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

Di Giallonardo F, Geoghegan JL, Docherty DE, McLean RG, Zody MC, Qu J, Yang X, Birren BW, Malboeuf CM, Newman RM, Ip HS, Holmes EC.

J Virol. 2015 Oct 28;90(2):862-72. doi: 10.1128/JVI.02305-15.

6.

Within-host whole-genome deep sequencing and diversity analysis of human respiratory syncytial virus infection reveals dynamics of genomic diversity in the absence and presence of immune pressure.

Grad YH, Newman R, Zody M, Yang X, Murphy R, Qu J, Malboeuf CM, Levin JZ, Lipsitch M, DeVincenzo J.

J Virol. 2014 Jul;88(13):7286-93. doi: 10.1128/JVI.00038-14.

7.

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

Li JZ, Chapman B, Charlebois P, Hofmann O, Weiner B, Porter AJ, Samuel R, Vardhanabhuti S, Zheng L, Eron J, Taiwo B, Zody MC, Henn MR, Kuritzkes DR, Hide W; ACTG A5262 Study Team., Wilson CC, Berzins BI, Acosta EP, Bastow B, Kim PS, Read SW, Janik J, Meres DS, Lederman MM, Mong-Kryspin L, Shaw KE, Zimmerman LG, Leavitt R, De La Rosa G, Jennings A.

PLoS One. 2014 Mar 6;9(3):e90485. doi: 10.1371/journal.pone.0090485.

8.

V-Phaser 2: variant inference for viral populations.

Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC.

BMC Genomics. 2013 Oct 3;14:674. doi: 10.1186/1471-2164-14-674.

9.

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.

Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD.

Nucleic Acids Res. 2013 Aug;41(14):e142. doi: 10.1093/nar/gkt481.

10.

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hůlková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ.

Nat Genet. 2013 Mar;45(3):299-303. doi: 10.1038/ng.2543.

11.

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR.

J Infect Dis. 2013 Jul;208(1):17-31. doi: 10.1093/infdis/jis679.

12.

De novo assembly of highly diverse viral populations.

Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR.

BMC Genomics. 2012 Sep 13;13:475. doi: 10.1186/1471-2164-13-475.

13.

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.

Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ.

Nucleic Acids Res. 2013 Jan 7;41(1):e13. doi: 10.1093/nar/gks794.

14.

Novel origins of copy number variation in the dog genome.

Berglund J, Nevalainen EM, Molin AM, Perloski M; LUPA Consortium., André C, Zody MC, Sharpe T, Hitte C, Lindblad-Toh K, Lohi H, Webster MT.

Genome Biol. 2012 Aug 23;13(8):R73. doi: 10.1186/gb-2012-13-8-r73.

15.

The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility.

Imsland F, Feng C, Boije H, Bed'hom B, Fillon V, Dorshorst B, Rubin CJ, Liu R, Gao Y, Gu X, Wang Y, Gourichon D, Zody MC, Zecchin W, Vieaud A, Tixier-Boichard M, Hu X, Hallböök F, Li N, Andersson L.

PLoS Genet. 2012 Jun;8(6):e1002775. doi: 10.1371/journal.pgen.1002775.

16.

Structural haplotypes and recent evolution of the human 17q21.31 region.

Boettger LM, Handsaker RE, Zody MC, McCarroll SA.

Nat Genet. 2012 Jul 1;44(8):881-5. doi: 10.1038/ng.2334.

17.

Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing.

Itsara A, Vissers LE, Steinberg KM, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson RK, Jenkins RB, Veltman JA, Eichler EE.

Am J Hum Genet. 2012 Apr 6;90(4):599-613. doi: 10.1016/j.ajhg.2012.02.013.

18.

The genomic basis of adaptive evolution in threespine sticklebacks.

Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C; Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team., Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM.

Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944.

19.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR.

PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417.

20.

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM.

PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529.

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